Add pytest configuration and CI infrastructure to prevent module import errors

[Copilot]

Repository lacked test infrastructure, causing ModuleNotFoundError when importing from multi-project structure (GA_denoise_selector, Mamba-SSM-Denoise, GA_smoother_classic).

Changes

Test Configuration

• setup.cfg: Configures pytest pythonpath to include all project roots, enabling from src import datasets and from smoothers import SGParams without path manipulation
• tests/reflectance/test_dose_metadata.py: Sample test validating import resolution
• .gitignore: Excludes pytest cache, coverage reports, build artifacts

CI/CD

• .github/workflows/ci-audit.yml:
  • Matrix build on Python 3.10/3.11
  • Sets PYTHONPATH via environment and explicit export (belt-and-suspenders)
  • Runs quick-marked tests with coverage
  • Includes flake8/black/isort checks
  • Minimal contents: read permissions (addresses CodeQL alert)

Documentation

• README.md: Added testing section with quick start
• tests/README.md: Comprehensive testing guide

Example

# tests/reflectance/test_dose_metadata.py
def test_import_src_package():
    """Now works without ModuleNotFoundError"""
    from src import datasets  # Resolved via setup.cfg pythonpath
    assert datasets is not None

The pythonpath configuration in setup.cfg:

[tool:pytest]
pythonpath = 
    .
    GA_denoise_selector
    Mamba-SSM-Denoise/Track_H_cross_validation
    GA_smoother_classic

Original prompt

The following are identified issues causing failures in the repository workflows:

1. Import Error in Tests:

   • There is a module import issue found in the tests under the module tests/reflectance/test_dose_metadata.py, specifically on line 5.
   • Error Message: ModuleNotFoundError: No module named 'src'.
   • This occurs because Pytest is unable to recognize the src package due to the absence of the correct Python path configuration.

2. Git Submodule Error:

   • Fatal Error: fatal: No url found for submodule path 'external/workspaces/Reflectance' in .gitmodules.
   • The repository seems to have an improperly initialized Git submodule at external/workspaces/Reflectance.

Proposed Fixes:

1. Resolve the Import Error for Pytest:

   • Update the CI configuration to set the correct Python path before running tests.
   • Example Fix (in .github/workflows/ci-audit.yml):

     - name: Run tests
       run: |
         export PYTHONPATH=$PYTHONPATH:$(pwd)/src
         pytest tests -m "quick" --maxfail=1 --cov=src --cov-report=term --cov-report=html

   • Alternatively, a setup.cfg can be added to define the Python path:

     [tool.pytest.ini_options]
     pythonpath = src

2. Fixing Git Submodule:

   • Ensure the external/workspaces/Reflectance submodule is properly initialized:

     git submodule update --init --recursive

   • Double-check .gitmodules to ensure the submodule has a valid URL specified:

     [submodule "external/workspaces/Reflectance"]
       path = external/workspaces/Reflectance
       url = <URL-to-submodule>
     

3. General Cleanup:

   • Remove or fix references to broken submodules if they are no longer in use.

Once these updates are applied, rerun the CI workflows to confirm that the issues are resolved.

This pull request was created from Copilot chat.

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[Copilot]

Pull request overview

This PR introduces a basic but structured testing and CI setup across the multi-project repo so imports like from src import ... and from smoothers import ... work consistently in both local and GitHub Actions environments.

Changes:

• Added pytest configuration (setup.cfg), initial test scaffolding under tests/, and documentation for running and troubleshooting tests.
• Introduced a CI workflow (ci-audit.yml) that runs quick-marked tests with coverage on Python 3.10/3.11 and performs lint-like checks (flake8/black/isort).
• Updated .gitignore and root README.md to align with the new testing and CI setup and to ignore build/test artifacts.

Reviewed changes

Copilot reviewed 7 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/reflectance/test_dose_metadata.py	Adds import-validation and placeholder tests to confirm the new Python path configuration and quick test marker wiring.
tests/reflectance/__init__.py	Declares the reflectance tests package for clearer test organization.
tests/__init__.py	Marks the top-level tests directory as a package and documents its purpose.
tests/README.md	Documents test layout, how to run tests/coverage, and troubleshooting steps for import issues.
setup.cfg	Configures pytest (pythonpath, discovery, markers) and coverage across the multi-project structure.
README.md	Adds sections on projects, running tests, and Python path behavior for contributors.
.gitignore	Ignores Python/build/test artifacts, logs, data outputs, and future external/ content.
.github/workflows/ci-audit.yml	Defines CI jobs for tests with coverage and code quality checks on pushes and PRs.

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[Copilot]

This "quick" test currently only imports sys/os, prints the environment, and asserts that the imported modules are not None, which will virtually never fail in normal conditions and doesn’t actually validate that the configured PYTHONPATH includes your project paths. Consider replacing the debug print calls with assertions that specific expected paths (e.g., project roots) are present in sys.path or os.environ['PYTHONPATH'], so the test will fail if the path configuration regresses.

Suggested change

	# Verify Python path includes expected directories
	pythonpath_str = os.environ.get('PYTHONPATH', '')
	print(f"PYTHONPATH: {pythonpath_str}")
	print(f"sys.path: {sys.path}")
	assert sys is not None
	assert os is not None
	# Verify Python path includes expected project-related entries
	pythonpath_str = os.environ.get("PYTHONPATH", "")
	expected_markers = ("src", "smoothers")
	for marker in expected_markers:
	assert (
	any(marker in path_entry for path_entry in sys.path)
	or marker in pythonpath_str
	), f"Expected '{marker}' to be present in sys.path or PYTHONPATH for imports to work."

[Copilot]

In the troubleshooting section, the PYTHONPATH export command omits the GA_smoother_classic directory, whereas setup.cfg and the CI workflow both include it in the Python path. To keep guidance consistent and avoid confusing import issues for GA_smoother_classic, consider adding :$(pwd)/GA_smoother_classic to this example command.

Suggested change

	export PYTHONPATH=$PYTHONPATH:$(pwd):$(pwd)/GA_denoise_selector:$(pwd)/Mamba-SSM-Denoise/Track_H_cross_validation
	export PYTHONPATH=$PYTHONPATH:$(pwd):$(pwd)/GA_denoise_selector:$(pwd)/Mamba-SSM-Denoise/Track_H_cross_validation:$(pwd)/GA_smoother_classic

[Copilot]

mypy is installed here but not used in any subsequent step, which adds CI time and dependency surface without benefit. Either add a mypy check step or remove mypy from the install list to keep the workflow lean.

Suggested change

	pip install flake8 black isort mypy
	pip install flake8 black isort